|
| Status |
Public on Dec 01, 2011 |
| Title |
Control KCl roots - 2hours - repeat 1 |
| Sample type |
RNA |
| |
|
| Source name |
Control KCl roots - 2hours - repeat 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: roots
ecotype: Columbia
treatment: 5mM KCl on ONE side for 2 hours
|
| Treatment protocol |
We selected the 12-14 days old plants with balanced roots on both sides and they were transferred on 12x12cm segmented agar plates containing either 5mM KNO3 or 5mM KCl on both sides for the controls or 5mM KNO3 on one side and 5mM KCl on the other side for the split. These plates contained 60 ml of solid basal MS medium supplemented with 0.3mM sucrose. The KNO3 or KCl compartments were obtained by spreading concentrated KNO3 and KCl solution on the solid medium 24 hr before the experiments to allow diffusion of the solutions
|
| Growth protocol |
Plants are grown on a custom-made basal Murashige and Skoog solid medium (no nitrogen, no sucrose), supplemented with 0.5 mM NH4-succinate, 0.1mM KNO3 and 3mM sucrose. After 8-10 days, the primary root was cut below the first two lateral roots and roots still grown on these plates for 4 more days. Then, each plant with two main roots was transferred on individual 10x10 cm plates containing the same 40 ml solid medium supplemented with 0.5mM NH4+-succinate as the nitrogen source. The solid medium was divided in two compartments by a trench to allow the physical separation of the two roots.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were carried out on roots collected at 2 hours, 8 hours and 2 days after the beginning of the split-root treatment with TRIzol (Invitrogen)
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the IVT - labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 10 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is EukGE-WS2v4_450.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Data were processed using MAS5.0v
|
| |
|
| Submission date |
Jul 15, 2010 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Sandrine Ruffel |
| E-mail(s) |
sandrine0ruffel@gmail.com
|
| Phone |
2129954918
|
| URL |
http://coruzzilab.bio.nyu.edu/home/
|
| Organization name |
New York University
|
| Department |
Biology
|
| Lab |
Coruzzi
|
| Street address |
100 Washington Square East. 1009 Main Building
|
| City |
NYC |
| State/province |
NY |
| ZIP/Postal code |
10012 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE22966 |
A systemic view of coordinated root responses to NO3- heterogeneous environment in Arabidopsis |
|
| Relations |
| Reanalyzed by |
GSE118579 |
